Freestyle strokes not appearing in Cycles texture bake
I'm fairly certain that Freestyle is a post-process type of render which means that when it happens it's more like what happens in the Compositor or Photoshop/Gimp.

Even though the depth buffer can be captured as a flat image to help with 3D reconstruction, 
when you add detail to a flat rendered image like this, there is no information available for the parts of the model which are not seen by the camera.(back-facing)

So as a post-process, Freestyle can add lines to the edges of model but only so far as those edges are viewable by the camera that was used for the render.

We cannot: 
(i)   take a picture of a giraffe using a camera, 
(ii)  print the photo, 
(iii) and then turn the photo around to see the reverse side of the subject in a 2D picture. 

So far as Freestyle is concerned, the Cycles/BI Render is a 2D picture.  

Even if Freestyle was run after a Cycles bake job; 
it would still only be run after the texture bake has completed; just as it only runs after a camera render has taken place. 

It's post-process.

Instead, you can duplicate your model then add a Wireframe Modifier.  Selectively delete geometry.



Add an Emission Shader to the wireframe.



Now bake, 



You may also want to bake an Emission Mask so that a GLSL shader won't overwrite the glowing areas with Directional lighting.
Just make the model'White'(1.0,1.0,1.0) and make the Sky solid Black



The Blender Render(Internal) Settings for masks like this can be found in the Textures Tab next to Materials.  Various game engines can make use of masks in a similar way.  

Just make sure to add the Mask as the 4th channel(alpha) for Blender or else it may not be used by Emit, Specular, Exponent, etc...



If you would like the baked lines to be black instead of Emission, then just use a regular Diffuse Material and the Shadows/Occlusion should make the lines black.